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Yorodumi- PDB-1m6u: Crystal Structure of a Novel DNA-binding domain from Ndt80, a Tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6u | ||||||
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Title | Crystal Structure of a Novel DNA-binding domain from Ndt80, a Transcriptional Activator Required for Meiosis in Yeast | ||||||
Components | Ndt80 protein | ||||||
Keywords | TRANSCRIPTION ACTIVATOR / yeast protein / DNA-binding / meiosis | ||||||
Function / homology | Function and homology information nuclear chromosome / meiotic cell cycle / sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Montano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast Authors: Montano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M. | ||||||
History |
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Remark 999 | SEQUENCE THE DISCREPANCIES ARE PRESENT DUE TO ERRORS IN PCR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6u.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6u.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m6u_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 1m6u_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 1m6u_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1m6u_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6u ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6u | HTTPS FTP |
-Related structure data
Related structure data | 1m7uSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31307.455 Da / Num. of mol.: 2 / Fragment: DNA binding domain, residues 59-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Ndt80 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ / References: UniProt: P38830 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.78 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: lithium sulfate, citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: Montano, S.P., (2002) Acta Crystallogr., D58, 2127. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 25573 / Num. obs: 25573 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.13 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2128 / % possible all: 84.9 |
Reflection | *PLUS Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 84.9 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ndt80, pdb entry 1M7U Resolution: 2.3→19.96 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
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Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
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LS refinement shell | Resolution: 2.3→2.33 Å /
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.226 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 / Rfactor Rwork: 0.33 |